Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Nucleosomes consist of approximately 146 bp of DNA wrapped around a histone octamer composed of pairs of each of the four core histones (H2A, H2B, H3, and H4). The chromatin fiber is further compacted through the interaction of a linker histone, H1, with the DNA between the nucleosomes to form higher order chromatin structures. This gene is intronless and encodes a replication-dependent histone that is a member of the histone H2B family. Two transcripts that encode the same protein have been identified for this gene, which is found in the large histone gene cluster on chromosome 6p22-p21.3. [provided by RefSeq, Aug 2015]
Transcription factors with Perturb-seq knockdown data for H2BC5. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = H2BC5 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.
| TF | Mean coef | Binding | Outlier | TF→Gene link |
|---|
Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of H2BC5, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.
| Accessibility | Element | Dist. to TSS | Link type | TFs |
|---|---|---|---|---|
| chr6:25,882,032–25,882,516 | 275.8 kb | Distal (>10kb) Multiome | 165 | |
| chr6:25,992,391–25,993,479 | 165.4 kb | Distal (>10kb) Multiome | 1012 | |
| chr6:26,020,104–26,022,401 | 137.8 kb | Distal (>10kb) Multiome | 920 | |
| chr6:26,025,866–26,027,859 | 131.8 kb | Distal (>10kb) Multiome | 1194 | |
| chr6:26,031,341–26,032,990 | 126.0 kb | Distal (>10kb) Multiome | 1083 | |
| chr6:26,033,113–26,034,309 | 124.5 kb | Distal (>10kb) Multiome | 800 | |
| chr6:26,054,926–26,057,287 | 102.8 kb | Distal (>10kb) Multiome | 1174 | |
| chr6:26,087,383–26,088,017 | 70.4 kb | Distal (>10kb) Multiome | 572 | |
| chr6:26,103,452–26,105,109 | 54.2 kb | Distal (>10kb) Multiome | 1169 | |
| chr6:26,122,481–26,124,909 | 35.2 kb | Distal (>10kb) Multiome HiCAR | 1216 | |
| chr6:26,125,788–26,126,592 | 31.9 kb | Distal (>10kb) Multiome HiCAR | 670 | |
| chr6:26,155,789–26,155,897 | 2.2 kb | Proximal (<10kb) | 108 | |
| chr6:26,156,184–26,158,744 | 51 bp | At TSS Multiome | 1310 | |
| chr6:26,159,281–26,159,626 | 1.2 kb | Proximal (<10kb) | 245 | |
| chr6:26,171,798–26,172,499 | 13.9 kb | Distal (>10kb) Multiome | 580 | |
| chr6:26,183,128–26,184,377 | 25.6 kb | Distal (>10kb) Multiome | 311 | |
| chr6:26,187,874–26,189,538 | 31.0 kb | Distal (>10kb) Multiome | 1053 | |
| chr6:26,196,695–26,197,676 | 39.2 kb | Distal (>10kb) Multiome | 842 | |
| chr6:26,198,203–26,200,197 | 41.3 kb | Distal (>10kb) Multiome | 939 | |
| chr6:26,203,791–26,205,119 | 46.3 kb | Distal (>10kb) Multiome | 1071 | |
| chr6:26,214,872–26,218,468 | 58.7 kb | Distal (>10kb) Multiome | 1096 | |
| chr6:26,223,716–26,224,480 | 65.9 kb | Distal (>10kb) Multiome | 507 | |
| chr6:26,224,856–26,226,566 | 67.1 kb | Distal (>10kb) Multiome | 451 | |
| chr6:26,239,944–26,240,920 | 82.2 kb | Distal (>10kb) Multiome | 375 | |
| chr6:26,249,682–26,251,138 | 92.2 kb | Distal (>10kb) Multiome | 731 | |
| chr6:26,251,339–26,252,079 | 93.6 kb | Distal (>10kb) Multiome | 445 | |
| chr6:26,270,815–26,273,967 | 114.8 kb | Distal (>10kb) Multiome | 742 | |
| chr6:26,285,011–26,286,121 | 127.4 kb | Distal (>10kb) Multiome | 1121 | |
| chr6:26,304,972–26,305,585 | 147.3 kb | Distal (>10kb) Multiome | 586 | |
| chr6:26,312,505–26,313,475 | 154.9 kb | Distal (>10kb) Multiome | 896 | |
| chr6:26,322,092–26,323,232 | 164.5 kb | Distal (>10kb) Multiome | 811 | |
| chr6:26,327,476–26,328,318 | 170.0 kb | Distal (>10kb) Multiome | 716 | |
| chr6:26,341,545–26,342,139 | 183.7 kb | Distal (>10kb) Multiome | 716 | |
| chr6:26,365,073–26,365,647 | 207.2 kb | Distal (>10kb) Multiome | 587 | |
| chr6:26,382,957–26,383,951 | 225.1 kb | Distal (>10kb) Multiome | 448 | |
| chr6:26,421,258–26,421,866 | 263.3 kb | Distal (>10kb) Multiome | 473 | |
| chr6:26,457,390–26,458,395 | 299.8 kb | Distal (>10kb) Multiome | 525 | |
| chr6:27,131,467–27,132,107 | 973.6 kb | Distal (>10kb) Multiome HiCAR | 580 | |
| chr6:27,132,200–27,134,276 | 974.8 kb | Distal (>10kb) Multiome HiCAR | 975 | |
| chr6:27,139,091–27,140,128 | 981.3 kb | Distal (>10kb) Multiome HiCAR | 662 | |
| chr6:27,145,480–27,148,111 | 988.9 kb | Distal (>10kb) Multiome HiCAR | 951 | |
| chr6:27,772,302–27,773,105 | 1614.6 kb | Distal (>10kb) Multiome HiCAR | 784 | |
| chr6:27,809,816–27,810,576 | 1652.0 kb | Distal (>10kb) Multiome HiCAR | 914 | |
| chr6:27,813,688–27,816,146 | 1656.8 kb | Distal (>10kb) Multiome HiCAR | 564 | |
| chr6:27,836,792–27,839,128 | 1680.3 kb | Distal (>10kb) Multiome HiCAR | 1131 | |
| chr6:27,865,093–27,868,152 | 1707.2 kb | Distal (>10kb) Multiome HiCAR | 744 | |
| chr6:27,870,957–27,872,527 | 1714.1 kb | Distal (>10kb) Multiome HiCAR | 426 | |
| chr6:27,872,808–27,873,995 | 1715.5 kb | Distal (>10kb) Multiome HiCAR | 372 |
Genomic view of the H2BC5 locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.